Contents

Jupyter Notebook files

Use minnie_plotly_and_vtk_visualizer.ipynb to generate a 2D and 3D interactive views of one or more cells of interest from the minnie mm^3 volume. Uses matplotlib, plotly, and vtk/openGL visualization methods. See an example visualization below.

vtk visualization of neurons in the minnie volume

Use aibs_metamodel_celltypes_v661_v2_layer_positions.ipynb to filter root ids of interest by cell classification (excitatory and inhibitory), and subclasses, such as layer location for pyramidal neurons and connectivity type for interneurons.

See chandelier folder for visualization notebooks and renderings of select Chandelier cells in the volume, highlighting the synaptic sites on to the initial axon segment of target pyramidal neurons.

Chandelier-target neuron rendering

Use pyvista_decimate_mesh_cell_bodies_minnie.ipynb to decimate cell meshes from the minnie volume. Default decimation setting is 95%. You must first download the meshes to your local drive using the minnie_plotly_and_vtk_visualizer.ipynb notebook. Decimated files will be saved in the ‘/dec’ subdirectory. Note that astrocyte meshes may take several hours to decimate. Most other cell types will only take minutes.

Use vtk_decimated_cell_meshes_minnie.ipynb to generate a 3D interactive view of one or more cells of interest using decimated meshes from the minnie mm^3 volume. Uses vtk/openGL and has a save view function. See an example visualization below.

vtk visualization of decimated meshes of astrocytes, neurons, and vascular cells in the minnie volume